3NEZ

mRojoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Generation of longer emission wavelength red fluorescent proteins using computationally designed libraries.

Chica, R.A.Moore, M.M.Allen, B.D.Mayo, S.L.

(2010) Proc Natl Acad Sci U S A 107: 20257-20262

  • DOI: 10.1073/pnas.1013910107
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The longer emission wavelengths of red fluorescent proteins (RFPs) make them attractive for whole-animal imaging because cells are more transparent to red light. Although several useful RFPs have been developed using directed evolution, the quest for ...

    The longer emission wavelengths of red fluorescent proteins (RFPs) make them attractive for whole-animal imaging because cells are more transparent to red light. Although several useful RFPs have been developed using directed evolution, the quest for further red-shifted and improved RFPs continues. Herein, we report a structure-based rational design approach to red-shift the fluorescence emission of RFPs. We applied a combined computational and experimental approach that uses computational protein design as an in silico prescreen to generate focused combinatorial libraries of mCherry mutants. The computational procedure helped us identify residues that could fulfill interactions hypothesized to cause red-shifts without destabilizing the protein fold. These interactions include stabilization of the excited state through H-bonding to the acylimine oxygen atom, destabilization of the ground state by hydrophobic packing around the charged phenolate, and stabilization of the excited state by a π-stacking interaction. Our methodology allowed us to identify three mCherry mutants (mRojoA, mRojoB, and mRouge) that display emission wavelengths > 630 nm, representing red-shifts of 20-26 nm. Moreover, our approach required the experimental screening of a total of ∼5,000 clones, a number several orders of magnitude smaller than those previously used to achieve comparable red-shifts. Additionally, crystal structures of mRojoA and mRouge allowed us to verify fulfillment of the interactions hypothesized to cause red-shifts, supporting their contribution to the observed red-shifts.


    Related Citations: 
    • Generation of Longer Emission Wavelength Red Fluorescent Proteins Using Computationally Designed Libraries
      Chica, R.A., Moore, M.M., Allen, B.D., Mayo, S.L.
      () To be published --: --

    Organizational Affiliation

    Division of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
mRojoA
A, B, C, D
242Discosoma sp.Mutation(s): 1 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CH6
Query on CH6
A,B,C,D
L-PEPTIDE LINKINGC16 H19 N3 O4 SMET,TYR,GLY
NRQ
Query on NRQ
A,B,C,D
L-PEPTIDE LINKINGC16 H17 N3 O4 SMET,TYR,GLY
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.24α = 90
b = 97.41β = 95.54
c = 84.16γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-01-08
    Changes: Database references
  • Version 1.3: 2015-03-04
    Changes: Derived calculations
  • Version 1.4: 2017-11-08
    Changes: Advisory, Refinement description